Subject: Energy minimization after docking

From: Pearl Zheng <[email-masked]>
Date: Thu, 23 Jan 2003 16:51:06 -0600 (CST)

Dear CCLer,

   Recently I want to perform energy minimization on the "best" predicted 
 docked structures to refine the orientation of the substrate in the 
 receptor site and to find the local energy minimum of the inhibitor-enzyme 
 interaction.

 Does anyone know how to use the Sybyl(Tripos) or 
FirstDiscovery(Schrodinger) to do this simulation? 
I will summarize the suggestions on the list.

> 
> Emilio X. E. ( J. Molecular Graphics and Modelling 18, 283-289, 2000) has 
> conducted energy minimization after docking. Their method was: the side 
> chains of the active site and the inhibitor were allowed to relax while 
> the rest of the receptor including the backbone of the active site were 
> fixed. 
> 

Thanks,

Mingzhu
-- 
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   Mingzhu Zheng

   Department of chemistry
   Southern Methodist University
   Dallas, TX 75275

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